7AAU | pdb_00007aau

Crystal structure of nitrosoglutathione reductase from Chlamydomonas reinhardtii in complex with NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.226 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.178 (Depositor) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structural and functional insights into nitrosoglutathione reductase from Chlamydomonas reinhardtii.

Tagliani, A.Rossi, J.Marchand, C.H.De Mia, M.Tedesco, D.Gurrieri, L.Meloni, M.Falini, G.Trost, P.Lemaire, S.D.Fermani, S.Zaffagnini, M.

(2020) Redox Biol 38: 101806-101806

  • DOI: https://doi.org/10.1016/j.redox.2020.101806
  • Primary Citation Related Structures: 
    7AAS, 7AAU, 7AV7

  • PubMed Abstract: 

    Protein S-nitrosylation plays a fundamental role in cell signaling and nitrosoglutathione (GSNO) is considered as the main nitrosylating signaling molecule. Enzymatic systems controlling GSNO homeostasis are thus crucial to indirectly control the formation of protein S-nitrosothiols. GSNO reductase (GSNOR) is the key enzyme controlling GSNO levels by catalyzing its degradation in the presence of NADH. Here, we found that protein extracts from the microalga Chlamydomonas reinhardtii catabolize GSNO via two enzymatic systems having specific reliance on NADPH or NADH and different biochemical features. Scoring the Chlamydomonas genome for orthologs of known plant GSNORs, we found two genes encoding for putative and almost identical GSNOR isoenzymes. One of the two, here named CrGSNOR1, was heterologously expressed and purified. Its kinetic properties were determined and the three-dimensional structures of the apo-, NAD + - and NAD + /GSNO-forms were solved. These analyses revealed that CrGSNOR1 has a strict specificity towards GSNO and NADH, and a conserved folding with respect to other plant GSNORs. The catalytic zinc ion, however, showed an unexpected variability of the coordination environment. Furthermore, we evaluated the catalytic response of CrGSNOR1 to thermal denaturation, thiol-modifying agents and oxidative modifications as well as the reactivity and position of accessible cysteines. Despite being a cysteine-rich protein, CrGSNOR1 contains only two solvent-exposed/reactive cysteines. Oxidizing and nitrosylating treatments have null or limited effects on CrGSNOR1 activity and folding, highlighting a certain resistance of the algal enzyme to redox modifications. The molecular mechanisms and structural features underlying the response to thiol-based modifications are discussed.


  • Organizational Affiliation
    • Department of Pharmacy and Biotechnologies, University of Bologna, I-40126, Bologna, Italy; CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, UMR8226, F-75005, Paris, France.

Macromolecule Content 

  • Total Structure Weight: 249.26 kDa 
  • Atom Count: 18,798 
  • Modeled Residue Count: 2,263 
  • Deposited Residue Count: 2,268 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
S-(hydroxymethyl)glutathione dehydrogenase
A, B, C, D, E
A, B, C, D, E, F
378Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: CHLRE_12g543400v5
EC: 1.1.1.284
UniProt
Find proteins for A0A2K3D6R4 (Chlamydomonas reinhardtii)
Explore A0A2K3D6R4 
Go to UniProtKB:  A0A2K3D6R4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2K3D6R4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
(Subject of Investigation/LOI)

Query on NAD



Download:Ideal Coordinates CCD File
BA [auth D]
HA [auth E]
I [auth A]
MA [auth F]
P [auth B]
BA [auth D],
HA [auth E],
I [auth A],
MA [auth F],
P [auth B],
U [auth C]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
CA [auth D]
DA [auth D]
EA [auth D]
IA [auth E]
J [auth A]
CA [auth D],
DA [auth D],
EA [auth D],
IA [auth E],
J [auth A],
JA [auth E],
K [auth A],
L [auth A],
M [auth A],
NA [auth F],
OA [auth F],
Q [auth B],
R [auth B],
V [auth C],
W [auth C]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
AA [auth D]
FA [auth E]
G [auth A]
GA [auth E]
H [auth A]
AA [auth D],
FA [auth E],
G [auth A],
GA [auth E],
H [auth A],
KA [auth F],
LA [auth F],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
Z [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
PA [auth F],
QA [auth F],
X [auth C],
Y [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
RA [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.226 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.178 (Depositor) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.754α = 90
b = 142.723β = 90
c = 206.587γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentItalyAlma Idea 2017 Program
Agence Nationale de la Recherche (ANR)France17-CE05-0001

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-30
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description